Is there a cost difference between Crushing Attack being metal balls (magnetism deflects) or ice balls (fire.melts) in terms of having special counters?

Not really.

In the case of powers where there are feasible mundane countermeasures, there is a limitation for that, normally -5%, but it's unlikely to apply to many innate attacks.

In neither case are those counters reasonably mundane. Or even especially realistic - the intensity of magnetic fields you would need to deflect something fast and heavy enough to count as an attack enough to miss a person sized target would be fairly ridiculous, and the rate of heat transfer you'd need to melt a ball of ice that counted as an attack might be physically impossible - the heat conductivity of the ice likely isn't high enough for it to melt in a fraction of a second even if you opened a gate to the sun or something.